SNP6 Copy number analysis (GISTIC2)
Adrenocortical Carcinoma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1VM4B7T
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1VM4B7T
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.22 (Firehose task version: 140).

Summary

There were 90 tumor samples used in this analysis: 23 significant arm-level results, 19 significant focal amplifications, and 27 significant focal deletions were found.

Results
Focal results

Figure 1. Genomic positions of amplified regions: the X-axis represents the normalized amplification signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 1. Get Full Table Amplifications Table - 19 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
5p15.33 | 2.1179e-08 | 2.1179e-08 | chr5:1288616-1300024 | 1
5q35.3 | 0.00020364 | 0.00020364 | chr5:176723780-176833588 | 11
12q14.1 | 0.0043919 | 0.0043919 | chr12:58080141-58481453 | 14
16q22.1 | 0.004052 | 0.0051993 | chr16:69367997-69491844 | 5
Xq28 | 0.0114 | 0.0114 | chrX:151841230-152714951 | 26
17q25.3 | 0.014283 | 0.014283 | chr17:79999378-80024315 | 3
19p13.12 | 0.020068 | 0.020068 | chr19:15293986-16628163 | 36
4p16.3 | 0.022386 | 0.022386 | chr4:1-2496016 | 50
14q11.2 | 0.032075 | 0.032075 | chr14:21010467-23970250 | 173
19q12 | 0.04544 | 0.04544 | chr19:30245583-30385544 | 1
Xp11.22 | 0.075299 | 0.075299 | chrX:53242630-53465013 | 5
1q22 | 0.077256 | 0.077256 | chr1:120523956-155499256 | 287
6q24.3 | 0.10369 | 0.10369 | chr6:147060843-148023227 | 3
9q31.3 | 0.12028 | 0.12028 | chr9:114596042-114618032 | 0 [C9orf84]
16q24.2 | 0.075299 | 0.12028 | chr16:87736713-88204631 | 5
6p21.31 | 0.19557 | 0.19557 | chr6:36197374-36214490 | 2
4q35.1 | 0.22208 | 0.22208 | chr4:19216059-191154276 | 779
16p13.3 | 0.22723 | 0.22723 | chr16:1-5327725 | 217
7p22.1 | 0.2356 | 0.2356 | chr7:1-24087697 | 154

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p15.33.

Table S1. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
TERT

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q35.3.

Table S2. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
NSD1
RN7SL562P
F12
GRK6
SLC34A1
RGS14
LMAN2
PRELID1
RAB24
MXD3
PFN3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q14.1.

Table S3. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CDK4
RN7SKP65
MIR26A2
CYP27B1
METTL1
TSPAN31
TSFM
CTDSP2
AVIL
OS9
METTL21B
XRCC6BP1
MARCH9
AGAP2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16q22.1.

Table S4. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
COG8
TERF2
NIP7
CYB5B
TMED6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq28.

Table S5. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL667P
snoU13|ENSG00000239037.1
PNMA6B
PNMA6D
PNMA6A
RN7SL190P
CETN2
CSAG2
CSAG4
MAGEA2B
CSAG3
MAGEA1
MAGEA2
MAGEA3
MAGEA6
MAGEA12
ZNF185
ZNF275
TREX2
PNMA3
NSDHL
HAUS7
PNMA5
ZFP92
CSAG1
PNMA6C

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.3.

Table S6. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
DUS1L
GPS1
RFNG

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.12.

Table S7. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
TPM4
BRD4
RN7SL844P
RAB8A
LINC00661
UCA1
CYP4F24P
CYP4F8
CYP4F23P
CYP4F3
NOTCH3
CYP4F2
AP1M1
AKAP8
KLF2
FAM32A
OR10H3
OR10H2
OR10H1
AKAP8L
CYP4F11
EPS15L1
WIZ
RASAL3
CYP4F12
EPHX3
C19orf44
HSH2D
PGLYRP2
CIB3
CALR3
CYP4F22
OR10H4
LINC00905
OR10H5
MIR1470

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4p16.3.

Table S8. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FGFR3
WHSC1
RN7SL589P
MIR943
SCARNA22
RN7SL671P
SNORA48|ENSG00000212458.1
TMED11P
RN7SL358P
ZNF721
ABCA11P
MIR571
ZNF141
ZNF732
ZNF876P
ZNF718
ZNF595
ATP5I
CTBP1
DGKQ
GAK
IDUA
LETM1
MYL5
PDE6B
RNF4
NELFA
SLBP
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
FGFRL1
PIGG
UVSSA
ZFYVE28
HAUS3
MFSD7
TMEM175
TMEM129
FAM53A
CRIPAK
RNF212
NAT8L
POLN
C4orf48
MIR4800

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q11.2.

Table S9. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
MIR208B
MIR208A
PABPN1
C14orf164
SNORA73|ENSG00000252114.1
SNORD41|ENSG00000212302.1
OR6J1
TRAC
TRAJ1
TRAJ2
TRAJ3
TRAJ4
TRAJ5
TRAJ6
TRAJ7
TRAJ8
TRAJ9
TRAJ10
TRAJ11
TRAJ12
TRAJ13
TRAJ14
TRAJ16
TRAJ17
TRAJ18
TRAJ19
TRAJ20
TRAJ21
TRAJ22
TRAJ23
TRAJ24
TRAJ25
TRAJ26
TRAJ27
TRAJ28
TRAJ29
TRAJ30
TRAJ31
TRAJ32
TRAJ33
TRAJ34
TRAJ35
TRAJ36
TRAJ37
TRAJ38
TRAJ39
TRAJ40
TRAJ41
TRAJ42
TRAJ43
TRAJ44
TRAJ45
TRAJ46
TRAJ47
TRAJ48
TRAJ49
TRAJ50
TRAJ52
TRAJ53
TRAJ54
TRAJ56
TRAJ57
TRAJ58
TRAJ59
TRAJ61
TRDV3
TRDC
TRDJ3
TRDJ2
TRDJ4
TRDJ1
TRDD3
TRDD2
TRDD1
TRDV2
TRAV41
TRAV40
TRAV39
TRAV36DV7
TRAV35
TRAV34
TRAV30
TRAV29DV5
TRAV27
TRAV25
TRAV24
TRDV1
TRAV23DV6
TRAV22
TRAV21
TRAV20
TRAV19
TRAV18
TRAV17
TRAV16
TRAV14DV4
TRAV10
TRAV7
TRAV6
TRAV5
TRAV4
TRAV3
TRAV2
RN7SL650P
SNORD8
SNORD9
LINC00641
RNASE8
RN7SL189P
ANG
BCL2L2
CEBPE
DAD1
HNRNPC
MMP14
MYH6
MYH7
OXA1L
PSMB5
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
SLC7A7
TOX4
EFS
PRMT5
EDDM3A
SUPT16H
ACIN1
SLC7A8
NGDN
LRP10
OR10G3
OR10G2
OR4E2
SLC39A2
ZNF219
SLC22A17
HAUS4
C14orf119
RBM23
ARHGEF40
METTL3
RPGRIP1
NDRG2
HOMEZ
CHD8
C14orf93
ABHD4
EDDM3B
CDH24
METTL17
IL25
RNASE7
RAB2B
AJUBA
PPP1R3E
CMTM5
RNASE11
TPPP2
MRPL52
PSMB11
REM2
OR6S1
RNASE9
OR5AU1
RNASE13
RNASE12
TMEM253
MIR4707

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q12.

Table S10. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CCNE1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp11.22.

Table S11. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
KDM5C
HSD17B10
SMC1A
IQSEC2
RIBC1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q22.

Table S12. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ARNT
BCL9
MUC1
NOTCH2
TPM3
PDE4DIP
snoU13|ENSG00000238805.1
MIR555
GBAP1
EFNA3
MIR4258
SNORD59|ENSG00000252682.1
SNORA58|ENSG00000201129.1
C1orf189
RN7SL431P
MIR5698
U3|ENSG00000252669.1
snoU13|ENSG00000238511.1
RN7SL372P
RN7SL44P
S100A7L2
SPRR2B
SNORA31|ENSG00000252920.1
LINC00302
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13|ENSG00000238526.1
RN7SL480P
OTUD7B
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
ADAR
CHRNB2
CKS1B|ENSG00000173207.8
CLK2
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
FCGR1A
FDPS
FLG
FMO5
GBA
GJA5
GJA8
IL6R
ILF2
IVL
KCNN3
LOR
MCL1
SMCP
MTX1
NPR1
PDZK1
PI4KB
PKLR
PRKAB2
PSMB4
PSMD4
RAB13
RFX5
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
THBS3
TCHH
TUFT1
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
ADAM15
PEX11B
SELENBP1
PRPF3
CHD1L
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SCAMP3
SF3B4
PIAS3
HAX1
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
JTB
MTMR11
SLC27A3
TDRKH
CD160
VPS45
POGZ
RPRD2
SNAPIN
RUSC1
CA14
NBPF14
C1orf43
CHTOP
LCE2B
SLC39A1
TMOD4
CERS2
CRNN
BOLA1
ZBTB7B
APH1A
PLEKHO1
GPR89B
OAZ3
DPM3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
UBE2Q1
FAM63A
ASH1L
LENEP
SLC50A1
CDC42SE1
PGLYRP4
ATP8B2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
HCN3
PRUNE
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
TRIM46
TARS2
FLAD1
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
AQP10
PYGO2
NUP210L
PGLYRP3
GABPB2
TCHHL1
RPTN
TDRD10
SHE
DCST2
LIX1L
S100A16
CREB3L4
C1orf51
HFE2
ANKRD35
NBPF12
LELP1
DCST1
BNIPL
SPRR4
PPIAL4A
LCE4A
NBPF11
KRTCAP2
CRTC2
LCE5A
RIIAD1
THEM5
NBPF16
ANKRD34A
HIST2H2AB
S100A7A
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
NOTCH2NL
LYSMD1
HRNR
FLG2
NBPF9
HIST2H2BF
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
MIR92B
HIST2H2AA4
FAM72D
GPR89C
MIR190B
C1orf68
C2CD4D
NBPF20
MIR4257

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q24.3.

Table S13. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
STXBP5
ADGB
SAMD5

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16q24.2.

Table S14. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FLJ00104
CA5A
SLC7A5
KLHDC4
BANP

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.31.

Table S15. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BRPF3
PNPLA1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q35.1.

Table S16. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
IL2
KDR
KIT
PDGFRA
RAP1GDS1
PHOX2B
DUX4
CHIC2
TET2
FBXW7
FIP1L1
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31|ENSG00000253013.1
TLR3
snoU13|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
snoU13|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51|ENSG00000201516.1
SCRG1
HMGB2
MIR548T
RN7SL253P
RNU6ATAC13P
HSP90AA6P
RNY4P17
SNORA51|ENSG00000207171.1
snoU13|ENSG00000238744.1
RN7SKP188
RN7SL776P
RNA5SP171
RNA5SP170
MIR578
TMEM192
RN7SKP105
U3|ENSG00000251979.1
C4orf45
U3|ENSG00000271817.1
PDGFC
FGB
TLR2
RN7SL419P
TMEM154
RN7SL446P
RNA5SP169
RN7SKP35
SNORD73A
SNORD73
RNA5SP168
RNA5SP167
RNA5SP166
RN7SL254P
MIR4799
RNA5SP165
TMEM184C
RN7SKP235
ANAPC10
HHIP
MIR3139
USP38
snoU13|ENSG00000238695.1
RN7SL152P
UCP1
SNORD112|ENSG00000252300.1
RN7SKP253
RN7SKP237
ACA64|ENSG00000239005.1
RN7SL311P
RN7SL382P
LINC00500
LINC00499
LINC00498
LINC00616
LINC00613
PCDH10
SNORA70|ENSG00000252014.1
RN7SL205P
RNY5P4
snoU13|ENSG00000238802.1
HSPA4L
INTU
RN7SL335P
QRFPR
RN7SKP137
MAD2L1
SNORA11|ENSG00000221245.1
C4orf3
CEP170P1
SNHG8
NT5C3AP1
MTRNR2L13
RN7SL808P
MIR577
RN7SL184P
TIFA
C4orf32
ENPEP
RN7SL275P
CCDC109B
MIR576
RN7SL55P
SNORD112|ENSG00000252566.1
GIMD1
RN7SL89P
SNORA31|ENSG00000252136.1
TACR3
BDH2
CISD2
snoU13|ENSG00000238948.1
RN7SL728P
MIR1255A
ADH1B
PCNAP1
MIR3684
EIF4E
RN7SKP28
RNA5SP164
RN7SKP248
GPRIN3
RN7SKP244
RNU6ATAC31P
IBSP
snoU13|ENSG00000238652.1
RN7SL681P
RN7SKP96
MIR4451
RN7SKP48
RN7SL552P
MRPS18C
snoR442|ENSG00000252834.1
MIR575
LINC00575
SNORD42|ENSG00000202440.1
HNRNPD
SNORA31|ENSG00000252762.1
SNORA75|ENSG00000212620.1
OR7E94P
LINC00989
NAA11
RN7SL127P
MIR5096
snoU13|ENSG00000238816.1
SNORD75|ENSG00000221711.1
MIR548AH
MIR4450
SNORD50|ENSG00000199857.1
CDKL2
BTC
PPBPP2
RN7SL218P
PPBP
PF4
PF4V1
SNORA3|ENSG00000221639.1
RNU6ATAC5P
RNU4ATAC9P
RNA5SP163
snoU13|ENSG00000238318.1
CSN1S2AP
SULT1B1
UGT2A1
UGT2A2
UGT2B10
TMPRSS11BNL
FTLP10
TMPRSS11GP
SNORA62|ENSG00000202374.1
GNRHR
UBA6
TECRL
snoU13|ENSG00000238925.1
snoU13|ENSG00000238541.1
snoU13|ENSG00000238579.1
NOA1
RN7SL357P
RN7SL492P
ARL9
SRP72
RNA5SP162
KIAA1211
RNA5SP161
RN7SKP30
RN7SL822P
RN7SL424P
snoU13|ENSG00000238753.1
GSX2
SNORA26|ENSG00000212490.1
SNORA26|ENSG00000212588.1
DANCR
snoU13|ENSG00000239068.1
NIPAL1
RN7SKP215
snoU13|ENSG00000238301.1
RN7SKP199
RN7SL193P
RN7SL691P
RN7SKP82
SLC30A9
LINC00682
RNA5SP160
snoU13|ENSG00000238351.1
RHOH
SNORA51|ENSG00000201863.1
RNA5SP159
RN7SL558P
SMIM14
MIR5591
RNA5SP158
DTHD1
snoU13|ENSG00000238694.1
RN7SL101P
SNORD74|ENSG00000200999.1
RN7SL16P
snoU13|ENSG00000238383.1
ADH1A
ADH1C
ADH4
ADH5
ADH6
ADH7
AFM
AFP
AGA
ALB
AMBN
ANK2
SLC25A4
ANXA3
ANXA5
APBB2
AREG
ART3
ATOH1
BMP3
BMPR1B
CAMK2D
CASP3
CASP6
CCKAR
CCNA2
CCNG2
SCARB2
LRBA
CDS1
CLGN
CENPC
CENPE
CLCN3
CNGA1
CPE
CSN1S1
CSN2
CSN3
CTSO
DCK
DCTD
DHX15
DMP1
DSPP
EDNRA
EGF
ELF2
EPHA5
EREG
ETFDH
F11
FABP2
ACSL1
FAT1
FGA
FGF2
FGF5
FGG
FRG1
GAB1
GABRA2
GABRA4
GABRB1
GABRG1
GC
GK2
GLRB
GPM6A
GRIA2
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
UBE2K
HPGD
HTN1
HTN3
CFI
IGFBP7
IGJ
RBPJ
IL8
IL15
ING2
CXCL10
IRF2
KLKB1
SMAD1
MANBA
MGST2
CXCL9
AFF1
NR3C2
MTNR1A
MTTP
MUC7
NDUFC1
NEK1
NFKB1
NPY1R
NPY2R
NPY5R
PCDH7
PDHA2
PET112
PITX2
PKD2
PLRG1
EXOSC9
POLR2B
POU4F2
PPEF2
PPAT
PPID
PPP3CA
PRKG2
MAPK10
PTPN13
REST
RFC1
ABCE1
RPL9
RPL34
RPS3A
MSMO1
CXCL6
CXCL11
CXCL5
SFRP2
SGCB
SNCA
SOD3
SPINK2
SPP1
STATH
SULT1E1
TDO2
TEC
TLL1
TLR1
TRPC3
TXK
UBE2D3
UCHL1
UGDH
UGT2B4
UGT2B7
UGT2B15
UGT2B17
UGT8
VEGFC
GLRA3
SPARCL1
SMARCA5
SORBS2
PRSS12
USO1
UNC5C
LAMTOR3
PDE5A
SLC4A4
SAP30
INPP4B
HERC3
PAPSS1
LRAT
AIMP1
NDST3
SLIT2
TMPRSS11D
ABCG2
HAND2
ADAMTS3
CLOCK
CEP135
RAPGEF2
MFAP3L
SEC24D
G3BP2
HNRNPDL
TSPAN5
ENAM
FAM13A
SPRY1
TLR6
ATP8A1
PGRMC2
SEC24B
CXCL13
SLC34A2
MAB21L2
PAICS
PDLIM5
RRH
CORIN
UGT2B11
PLK4
PTTG2
HPSE
NMU
SMR3B
NPFFR2
PPARGC1A
UGT2A1
CCNI
LIAS
ADAM29
PRDM5
LSM6
NUDT6
ANXA10
KLHL2
SEC31A
RUFY3
MMRN1
LIMCH1
WDFY3
PALLD
DCUN1D4
TBC1D9
METAP1
TBC1D1
SEL1L3
KIAA0922
PDS5A
LPHN3
TRIM2
SLC7A11
CCRN4L
PARM1
FAM149A
RCHY1
ANKRD17
STAP1
FBXO8
SMR3A
PPA2
DAPP1
DKK2
NAAA
COQ2
ARFIP1
HPGDS
ZNF330
TMPRSS11E
ZCCHC4
ANAPC4
SPOCK3
KLHL5
SEPSECS
COPS4
AADAT
HSD17B11
LEF1
HERC5
KLF3
FAM198B
PLAC8
LARP7
EMCN
MYOZ2
ASIC5
GALNT7
NUDT9
NUP54
CLDN22
GAR1
UGT2B28
RBM47
PCDH18
USP53
OTUD4
DCHS2
ARHGEF38
OCIAD1
COMMD8
ODAM
C4orf27
HERC6
MARCH1
BANK1
LARP1B
SDAD1
TMEM33
LGI2
BBS7
NEIL3
PGM2
C4orf19
TBC1D19
PI4K2B
TMEM144
TMA16
C4orf21
AP1AR
MAML3
CHRNA9
BMP2K
DDX60
CDKN2AIP
TENM3
N4BP2
SEPT11
EXOC1
LRP2BP
TMEM165
FSTL5
SMARCAD1
MEPE
STOX2
PRDM8
UTP3
INTS12
ANKRD50
ATP10D
RNF150
KIAA1239
KLHL8
KIAA1430
FNIP2
SLAIN2
SHROOM3
STIM2
SH3RF1
METTL14
WDR19
GBA3
ENOPH1
PROL1
OSTC
IL21
RXFP1
GUF1
SPCS3
SCOC
TRAPPC11
NEUROG2
SLC39A8
NDST4
ETNPPL
USP46
MRPL1
RASL11B
ELOVL6
NDNF
FAT4
ARSJ
SRD5A3
ARHGAP10
MLF1IP
THAP9
NSUN7
UGT2A3
GSTCD
MAP9
TNIP3
PHF17
SCD5
DNAJB14
TMEM156
WWC2
FRAS1
NAA15
CWH43
C4orf29
ALPK1
CXXC4
KCNIP4
CEP44
SETD7
PLA2G12A
TLR10
SLC25A31
RAB33B
ARHGAP24
SNX25
TTC29
MND1
SLC10A7
TKTL2
C4orf17
FAM175A
KIAA1109
HOPX
COL25A1
LNX1
MGARP
AGPAT9
CBR4
PIGY
CABS1
FHDC1
PRMT10
CCDC149
DDX60L
YTHDC1
NAF1
MOB1B
FAM114A1
TRMT10A
TBCK
HELQ
CYP2U1
DDIT4L
WDR17
ARAP2
PCAT4
ANTXR2
OCIAD2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
ZFP42
LIN54
SPATA18
TMPRSS11B
GNPDA2
SPATA4
AASDH
PDCL2
C4orf36
PACRGL
TRAM1L1
ENPP6
SLC9B2
ASB5
SLC9B1
ZNF827
SH3D19
NFXL1
PAQR3
SHISA3
SCFD2
FAM218A
THAP6
C4orf26
KLB
PPM1K
RASGEF1B
SPATA5
BBS12
DCLK2
GPR125
TRIM60
FREM3
MMAA
TIGD2
RASSF6
RBM46
SGMS2
COX7B2
SYNPO2
C4orf46
SLC10A4
TIGD4
RWDD4
CCDC111
TRIML2
CNOT6L
C4orf22
EPGN
ELMOD2
NPNT
CCDC110
MFSD8
FDCSP
NAP1L5
DCAF4L1
COX18
YIPF7
FRYL
RNF175
STPG2
ZAR1
CCDC158
TMPRSS11A
TRIML1
LRRC66
PRSS48
SOWAHB
LRIT3
SLC10A6
HSD17B13
ANKRD37
KCTD8
SMIM20
BEND4
GRXCR1
TMPRSS11F
TRIM61
HELT
C4orf40
AMTN
CCSER1
MIR302A
MTHFD2L
TMEM150C
GUSBP5
C4orf47
DUX4L4
GALNTL6
MIR302B
MIR302C
MIR302D
MIR367
FRG2
C4orf51
DUX4L7
DUX4L6
DUX4L5
DUX4L3
MIR573
MIR574
AREGB
DUX4L2
FAM160A1
RELL1
MIR297
FAM47E
CLDN24
MIR1269A
MIR1305
MIR548G
MIR3140
MIR4276
MIR3945
THEGL
MIR4455
MIR4453
MIR4802
MIR4801
MIR4449
MIR548AG1
MIR4452
FAM47E
MIR5705
PYURF

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p13.3.

Table S17. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CREBBP
TSC2
ALG1
RN7SL850P
DNASE1
CASP16
LINC00514
PRSS41
SNORA3|ENSG00000221719.1
PRSS27
PDPK2
ATP6C
ABCA17P
BRICD5
SNORD60|ENSG00000206630.1
MIR1225
RN7SL219P
NPW
SNHG9
SNORA64|ENSG00000207405.1
SNORA10
RPL3L
RN7SL367P
MIR3177
CCDC154
PRSS29P
C1QTNF8
MSLNL
METRN
MIR3176
MIR5587
ITFG3
HBZ
SNRNP25
POLR3K
WASIR2
WASH4P
DDX11L10
ABCA3
ADCY9
ARHGDIG
ATP6V0C
CCNF
CLCN7
ECI1
DNASE1L2
E4F1
GFER
HAGH
HBA1
HBA2
HBM
HBQ1
HMOX2
IGFALS
MEFV
MPG
NDUFB10
NME3
NME4
NTHL1
NTN3
OR1F1
OR2C1
PDPK1
PKD1
PPL
RPS2
SRL
CAPN15
SSTR5
TCEB2
TFAP4
TPSAB1
UBE2I
ZNF75A
ZNF174
ZNF200
ZNF205
ZNF213
NPRL3
AXIN1
RGS11
CACNA1H
BAIAP3
RHBDL1
CLDN6
CLDN9
PKMYT1
PIGQ
DNAJA3
SYNGR3
IL32
SLC9A3R2
SEC14L5
RAB11FIP3
IFT140
TELO2
NUBP2
ZNF263
TRAP1
MSLN
STUB1
MRPL28
TBL3
RNPS1
PRSS21
CLUAP1
MAPK8IP3
MGRN1
TPSD1
SRRM2
TPSG1
RAB26
ZNF500
DECR2
UBN1
CDIP1
SOX8
AMDHD2
PAM16
NAGPA
TNFRSF12A
MSRB1
GNG13
KCTD5
ZSCAN32
HCFC1R1
LUC7L
NMRAL1
TBC1D24
CASKIN1
CRAMP1L
RAB40C
TMEM8A
CHTF18
PRSS22
MLST8
RHBDF1
MMP25
NARFL
TPSB2
HS3ST6
PDIA2
UNKL
LMF1
FAM173A
MRPS34
THOC6
KREMEN2
CORO7
ROGDI
TMEM204
NAA60
C16orf59
FAHD1
ITFG3
WDR24
TRAF7
FLYWCH1
HAGHL
NUDT16L1
C16orf13
FAM195A
SLX4
GNPTG
GLYR1
GLIS2
ZSCAN10
RHOT2
ZNF598
HN1L
SPSB3
TIGD7
RPUSD1
FLYWCH2
VASN
TSR3
WFIKKN1
NOXO1
CCDC78
ZG16B
PRSS30P
PAQR4
ANKS3
UBALD1
SEPT12
RNF151
C16orf11
FBXL16
ZNF597
CCDC64B
C16orf89
C16orf71
FAM86A
WDR90
EME2
NLRC3
MEIOB
PRSS33
PGP
NHLRC4
C16orf91
JMJD8
C16orf96
PRR25
PTX4
SMIM22
C16orf90
MIR662
CEMP1
MIR940
MIR3178
MTRNR2L4
MIR3677
MIR4717
MIR4516

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p22.1.

Table S18. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ETV1
PMS2
CARD11
snoU13|ENSG00000238849.1
SNORD65|ENSG00000212264.1
MALSU1
SNORD93
RNA5SP227
MIR1183
RN7SL542P
SP8
SNORD56|ENSG00000200753.1
MIR3146
RN7SKP266
SNORA63|ENSG00000199473.1
ISPD
RN7SKP228
SNORA64|ENSG00000199470.1
TMEM106B
U3|ENSG00000212422.1
RPA3
PMS2CL
GRID2IP
FLJ20306
RN7SL851P
SNORA42|ENSG00000207217.1
RN7SL556P
ZNF815P
MIR589
snoU13|ENSG00000238394.1
ZNF890P
RNF216P1
AP5Z1
snoU13|ENSG00000238781.1
RN7SKP130
snoU13|ENSG00000238857.1
MIR4648
GRIFIN
MIR4655
ELFN1
UNCX
MIR339
COX19
FAM20C
ACTB
AHR
DGKB
GNA12
GPER
ICA1
IL6
ITGB8
LFNG
MEOX2
NUDT1
NDUFA4
PDGFA
PRKAR1B
RAC1
FSCN1
SP4
TWIST1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
DNAH11
CYTH3
PHF14
HDAC9
RAPGEF5
ARL4A
GPNMB
AGR2
IGF2BP3
KDELR2
ADAP1
NUPL2
SNX13
IQCE
SUN1
SOSTDC1
WIPI2
INTS1
TSPAN13
EIF2AK1
BZW2
SNX8
TRA2A
FTSJ2
NXPH1
GET4
CCZ1
MIOS
RNF216
TOMM7
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
CDCA7L
RADIL
KLHL7
STK31
PAPOLB
C1GALT1
ANKMY2
RBAK
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
FAM126A
FAM220A
SCIN
ZFAND2A
CCDC126
GLCCI1
GPR146
AMZ1
AGR3
TMEM184A
VWDE
PRPS1L1
TWISTNB
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
THSD7A
FERD3L
SLC29A4
RSPH10B
TMEM196
STEAP1B
COL28A1
ABCB5
FAM221A
MACC1
AGMO
OCM
RSPH10B2
ANKRD61
MIR3683
LRRC72
MIR4656

Figure 2. Genomic positions of deleted regions: the X-axis represents the normalized deletion signals (top) and significance by Q value (bottom). The green line represents the significance cutoff at Q value=0.25.

Table 2. Get Full Table Deletions Table - 27 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
22q12.1 | 1.5177e-26 | 1.5177e-26 | chr22:29192671-29455701 | 1
3q13.31 | 4.6428e-12 | 4.6428e-12 | chr3:116568608-116653900 | 2
4q35.1 | 3.949e-19 | 2.1938e-10 | chr4:183087331-184213557 | 6
1p36.23 | 5.8114e-09 | 5.8114e-09 | chr1:8403012-8925111 | 2
9p21.3 | 2.7993e-06 | 3.6042e-05 | chr9:21626574-22448737 | 5
13q14.2 | 0.00026571 | 0.00026571 | chr13:48875329-49064807 | 2
4q34.3 | 7.6683e-12 | 0.00062311 | chr4:179280062-182757119 | 4
9p23 | 0.0014894 | 0.002281 | chr9:8885227-12687261 | 2
17q24.2 | 0.0014894 | 0.0092911 | chr17:66075888-66865465 | 9
11p15.5 | 0.012075 | 0.012075 | chr11:1590306-1920254 | 9
2q37.3 | 0.027232 | 0.025834 | chr2:239359581-243199373 | 46
17q21.31 | 0.0039521 | 0.025834 | chr17:35750456-45000302 | 262
20p12.1 | 0.025834 | 0.025834 | chr20:1-18748064 | 175
16p13.3 | 0.036251 | 0.036251 | chr16:5144019-7780235 | 2
6q26 | 0.039612 | 0.038316 | chr6:161693099-169617013 | 33
11q14.1 | 0.042501 | 0.042483 | chr11:82995735-85567968 | 6
17q11.2 | 0.041396 | 0.042483 | chr17:29845106-29888119 | 3
16q23.1 | 0.053507 | 0.055824 | chr16:72807414-90354753 | 167
4q34.3 | 4.1389e-13 | 0.072215 | chr4:121980639-191154276 | 290
18q21.2 | 0.10216 | 0.10517 | chr18:48472083-48650073 | 3
7q36.3 | 0.10871 | 0.11632 | chr7:95210837-159138663 | 578
2q22.1 | 0.16089 | 0.16089 | chr2:101211503-143800397 | 231
6p24.3 | 0.17423 | 0.17943 | chr6:1-21599699 | 125
10q23.1 | 0.17943 | 0.17943 | chr10:1-135534747 | 991
14q21.2 | 0.17943 | 0.17943 | chr14:1-76821632 | 616
12q14.2 | 0.18438 | 0.18761 | chr12:56311604-92543184 | 237
1q43 | 0.23015 | 0.23015 | chr1:233111097-249250621 | 139

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q12.1.

Table S19. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ZNRF3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q13.31.

Table S20. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
LINC00901
MIR4447

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.1.

Table S21. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
DCTD
MIR1305

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.23.

Table S22. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
SNORA77|ENSG00000221083.1
RERE

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p21.3.

Table S23. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL151P
CDKN2A
CDKN2B
MTAP
C9orf53

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.2.

Table S24. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RB1
LPAR6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.3.

Table S25. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p23.

Table S26. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL5P
SNORD27|ENSG00000251699.1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.2.

Table S27. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PRKAR1A
FAM20A
MIR635
ARSG
LRRC37A16P
LINC00674
SLC16A6
AMZ2
WIPI1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.5.

Table S28. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
C11orf89
FAM99B
CTSD
LSP1|ENSG00000130592.9
TNNI2
SYT8
FAM99A
IFITM10
MIR4298

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.3.

Table S29. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
AGXT
KIF1A
BOK
DTYMK
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
HDAC4
FARP2
STK25
CAPN10
PASK
ATG4B
SNED1
ANO7
THAP4
ANKMY1
GAL3ST2
C2orf54
ING5
TWIST2
NEU4
MTERFD2
OTOS
MYEOV2
OR6B3
DUSP28
AQP12A
OR6B2
PRR21
AQP12B
D2HGDH
MIR4269
MIR4786

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q21.31.

Table S30. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RARA
BRCA1
ERBB2
ETV4
LASP1
MLLT6
RNU6ATAC3P
FAM215B
RN7SL199P
RN7SL656P
RN7SL739P
LRRC37A4P
RN7SL730P
RNA5SP443
MAP3K14
FAM187A
CCDC103
RN7SL405P
RN7SL819P
FZD2
RN7SL258P
GPATCH8
U3|ENSG00000221496.1
RN7SL507P
U3|ENSG00000221044.1
C17orf105
LINC00910
LINC00854
SNORA40|ENSG00000212149.1
RNY4P2
G6PC
AOC4P
CNTD1
CCR10
HSD17B1
MIR5010
MIR548AT
ZNF385C
TTC25
RN7SL871P
RN7SL399P
RNA5SP442
EIF1
KRT42P
LINC00974
KRT223P
KRT222
KRT222
RNA5SP441
GJD3
RNY4P8
SNORD124
IKZF3
MIR4728
PNMT
TCAP
NEUROD2
ARL5C
LINC00672
SNORA21|ENSG00000199293.1
SNORA21|ENSG00000252699.1
RPL23
RNA5SP440
CISD3
MIR4726
RN7SL102P
RN7SL458P
SOCS7
ACLY
AOC2
ARL4D
ATP6V0A1
FMNL1
CACNB1
CDC6
CCR7
CNP
CRHR1
CSF3
DHX8
DUSP3
EZH1
GAST
KAT2A
GFAP
GRB7
GRN
HCRT
IFI35
IGFBP4
ITGA2B
JUP
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
NBR1
MAPT
ADAM11
MEOX1
MPP2
MPP3
NAGLU
NMT1
NSF
MED1
PPY
PSMB3
PYY
PSMD3
RAB5C
RPL19
RPL27
SLC4A1
SMARCE1
STAT3
STAT5A
STAT5B
TADA2A
HNF1B
MLX
THRA
TOP2A
DNAJC7
TUBG1
UBTF
WNT3
WNT9B
PCGF2
RND2
PIP4K2B
CNTNAP1
AOC3
BECN1
KRT38
KRT37
KRT36
HAP1
EFTUD2
NR1D1
PLEKHM1
MED24
LRRC37A
HDAC5
GJC1
PSME3
NBR2
RAMP2
VAT1
LEPREL4
HEXIM1
C1QL1
RUNDC3A
STARD3
DDX52
DUSP14
SYNRG
CASC3
KCNH4
FAM215A
KRT23
TUBG2
NKIRAS2
COA3
PSMC3IP
SOST
RAPGEFL1
ARL17A
SLC25A39
HIGD1B
CDK12
KRT20
CWC25
KLHL11
GSDMB
ATXN7L3
PLXDC1
ARHGAP23
FKBP10
WNK4
C17orf53
TMUB2
DHX58
ACBD4
DCAKD
PLEKHH3
DBF4B
COASY
SRCIN1
AARSD1
PPP1R1B
TBC1D3F
MIEN1
MRPL45
VPS25
TMEM101
GHDC
TNS4
FBXL20
G6PC3
ASB16
PGAP3
HSPB9
ORMDL3
PLCD3
TMEM106A
NT5C3B
ZPBP2
SPATA32
HEXIM2
LSM12
CCDC43
KRT40
CD300LG
KIF18B
RUNDC1
WIPF2
KRT25
TMEM99
NAGS
FAM134C
SPPL2C
KRT28
KRT24
ARHGAP27
STH
KANSL1
FAM171A2
C17orf104
GSDMA
PTRF
KLHL10
MSL1
KRT27
LRRC37A11P
STAC2
KRT26
C17orf98
LINC00671
KRT39
GPR179
LRRC37A2
FBXO47
TBC1D3
C17orf96
MIR2117
LRRC3C
ARL17B
MIR4734
MIR4727
PTGES3L

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.1.

Table S31. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RNU6ATAC34P
RN7SL638P
LINC00493
MIR3192
RNA5SP476
RNY4P11
RN7SKP74
RN7SL14P
PET117
SNORD17
RN7SKP69
U3|ENSG00000212165.1
RNA5SP475
RN7SL864P
RN7SKP111
LINC00687
C20orf187
JAG1
RNU105B
TMX4
RN7SL547P
snoR26
RN7SL498P
LINC00654
LINC00658
SNORA26|ENSG00000212517.1
RNA5SP474
RN7SL514P
snoU13|ENSG00000252058.1
SNORA31|ENSG00000252096.1
MIR103A2
MAVS
U3|ENSG00000201346.1
RN7SL839P
RN7SL555P
TMEM239
SNORD57
SNORD56|ENSG00000229686.1
SNORD86
SNORA51|ENSG00000271798.1
SNORD110
MIR1292
SNORD119
RN7SL561P
TCF15
CSNK2A1
DEFB128
DEFB127
DEFB126
DEFB125
ADRA1D
JAG1
AVP
BFSP1
BMP2
CDC25B
CENPB
CHGB
FKBP1A
GNRH2
IDH3B
ITPA
OXT
PCNA
PCSK2
PDYN
PLCB4
PRNP
PTPRA
RRBP1
SIGLEC1
SNAP25
SNRPB
SNRPB2
SOX12
TGM3
ZNF133
MKKS
ATRN
CDS2
PSMF1
SNPH
LZTS3
RASSF2
SLC23A2
SIRPB1
SEC23B
NOP56
RBCK1
POLR3F
RBBP9
DSTN
RNF24
UBOX5
BTBD3
PLCB1
PRND
FLRT3
LAMP5
SPEF1
C20orf194
SDCBP2
SNX5
TMEM230
ANGPT4
ESF1
TRMT6
HAO1
SMOX
CRLS1
C20orf27
DZANK1
SPTLC3
AP5S1
TMEM74B
SIRPG
FERMT1
KIF16B
TASP1
NSFL1C
GPCPD1
CPXM1
OTOR
PAK7
EBF4
TRIB3
OVOL2
FASTKD5
ANKEF1
GFRA4
VPS16
PCED1A
MRPS26
DDRGK1
NDUFAF5
ZNF343
NRSN2
PANK2
ADAM33
SEL1L2
FAM110A
SLC4A11
MCM8
ZCCHC3
SCRT2
MGME1
DTD1
SLC52A3
HSPA12B
TMC2
TBC1D20
SIRPD
C20orf141
PROKR2
SLX4IP
C20orf96
MACROD2
SRXN1
BANF2
ISM1
DEFB129
SIRPA
STK35
PRNT
C20orf196
LRRN4
SIRPB2
RSPO4
TGM6
DEFB132
C20orf202
LINC00851
RAD21L1
TMEM239
CSRP2BP

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p13.3.

Table S32. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
SNORA40|ENSG00000252138.1
RBFOX1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q26.

Table S33. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FGFR1OP
MLLT4
TCP10
TTLL2
GPR31
MIR1913
SFT2D1
SNORD45|ENSG00000231297.2
LINC00473
SDIM1
RNA5SP226
RN7SL366P
CAHM
snoU13|ENSG00000239136.1
CCR6
KIF25
PARK2
RPS6KA2
T
RNASET2
QKI
PDE10A
C6orf123
MPC1
UNC93A
SMOC2
FRMD1
PACRG
DACT2
C6orf118
PRR18
TCP10L2
MIR3939

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q14.1.

Table S34. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
DLG2
SYTL2
TMEM126B
CREBZF
TMEM126A
CCDC89

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q11.2.

Table S35. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL45P
MIR193A
MIR4724

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.1.

Table S36. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CBFA2T3
FANCA
MAF
FAM157C
TUBB8P7
URAHP
TUBB3
SNORD68
SLC22A31
MIR4722
MIR5189
ZFPM1
ZNF469
FLJ00104
FBXO31
snoU13|ENSG00000239186.1
FENDRR
LINC00917
GINS2
RN7SL381P
LINC00311
TLDC1
RNA5SP433
KCNG4
RNA5SP432
MIR3182
RN7SL134P
snoU13|ENSG00000238321.1
RN7SKP190
7SK|ENSG00000260682.2
MIR4720
GAN
PKD1L2
CMC2
RNA5SP431
PIH1
MON1B
SNORD33|ENSG00000252022.1
RN7SKP233
RNA5SP430
RN7SL520P
ADAT1
CHST6
SNORA76|ENSG00000252122.1
GLG1
NPIPB15
HCCAT5
AFG3L1P
APRT
ZFHX3
C16orf3
CA5A
CDH13
CDH15
COX4I1
CTRB1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
HSBP1
HSD17B2
IRF8
KARS
MC1R
MVD
CHMP1A
PLCG2
PSMD7
RPL13
SPG7
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
VPS9D1
KIAA0513
PIEZO1
ATP2C2
CLEC3A
MPHOSPH6
EMC8
TUBB3
CFDP1
PRDM7
GABARAPL2
TCF25
ZCCHC14
GSE1
ATMIN
COTL1
MLYCD
CHST5
CPNE7
IL17C
ANKRD11
OSGIN1
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
DEF8
BANP
RFWD3
ZDHHC7
CENPN
JPH3
VAT1L
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNRF1
CNTNAP4
CENPBD1
ZNF276
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
SPATA33
ZC3H18
CDYL2
TMEM170A
SLC38A8
ADAD2
ZFP1
ADAMTS18
LDHD
MLKL
ZNF778
ACSF3
LINC00304
NUDT7
SNAI3
FAM92B
CTU2
C16orf47
PABPN1L
C16orf74
CTRB2
CLEC18B
SYCE1L
MIR1910
C16orf95
MIR4719
MIR5093

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.3.

Table S37. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
IL2
DUX4
FBXW7
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31|ENSG00000253013.1
TLR3
snoU13|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
snoU13|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51|ENSG00000201516.1
SCRG1
HMGB2
MIR548T
RN7SL253P
RNU6ATAC13P
HSP90AA6P
RNY4P17
SNORA51|ENSG00000207171.1
snoU13|ENSG00000238744.1
RN7SKP188
RN7SL776P
RNA5SP171
RNA5SP170
MIR578
TMEM192
RN7SKP105
U3|ENSG00000251979.1
C4orf45
U3|ENSG00000271817.1
PDGFC
FGB
TLR2
RN7SL419P
TMEM154
RN7SL446P
RNA5SP169
RN7SKP35
SNORD73A
SNORD73
RNA5SP168
RNA5SP167
RNA5SP166
RN7SL254P
MIR4799
RNA5SP165
TMEM184C
RN7SKP235
ANAPC10
HHIP
MIR3139
USP38
snoU13|ENSG00000238695.1
RN7SL152P
UCP1
SNORD112|ENSG00000252300.1
RN7SKP253
RN7SKP237
ACA64|ENSG00000239005.1
RN7SL311P
RN7SL382P
LINC00500
LINC00499
LINC00498
LINC00616
LINC00613
PCDH10
SNORA70|ENSG00000252014.1
RN7SL205P
RNY5P4
snoU13|ENSG00000238802.1
HSPA4L
INTU
RN7SL335P
QRFPR
RN7SKP137
AGA
SLC25A4
ANXA5
CASP3
CCNA2
LRBA
CLGN
CLCN3
CPE
CTSO
DCTD
EDNRA
ELF2
ETFDH
F11
ACSL1
FAT1
FGA
FGF2
FGG
FRG1
GAB1
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
HPGD
IL15
ING2
IRF2
KLKB1
SMAD1
MGST2
NR3C2
MTNR1A
NDUFC1
NEK1
NPY1R
NPY2R
NPY5R
PET112
PLRG1
EXOSC9
POU4F2
PPID
ABCE1
RPS3A
MSMO1
SFRP2
TDO2
TLL1
TRPC3
VEGFC
GLRA3
SMARCA5
SORBS2
SAP30
INPP4B
LRAT
HAND2
RAPGEF2
MFAP3L
SPRY1
PGRMC2
MAB21L2
PLK4
ADAM29
LSM6
NUDT6
ANXA10
KLHL2
PALLD
TBC1D9
KIAA0922
TRIM2
SLC7A11
CCRN4L
FAM149A
FBXO8
ARFIP1
ZNF330
SPOCK3
AADAT
FAM198B
ASIC5
GALNT7
CLDN22
PCDH18
OTUD4
DCHS2
C4orf27
MARCH1
LARP1B
BBS7
NEIL3
TMEM144
TMA16
MAML3
DDX60
CDKN2AIP
TENM3
LRP2BP
FSTL5
STOX2
ANKRD50
RNF150
KIAA1430
FNIP2
SH3RF1
IL21
RXFP1
SPCS3
SCOC
TRAPPC11
FAT4
ARHGAP10
MLF1IP
MAP9
TNIP3
PHF17
WWC2
NAA15
C4orf29
CEP44
SETD7
SLC25A31
RAB33B
SNX25
TTC29
MND1
SLC10A7
TKTL2
KIAA1109
MGARP
CBR4
FHDC1
PRMT10
DDX60L
NAF1
WDR17
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
ZFP42
SPATA4
ENPP6
ASB5
ZNF827
SH3D19
FAM218A
SPATA5
BBS12
DCLK2
TRIM60
FREM3
MMAA
RBM46
C4orf46
TIGD4
RWDD4
CCDC111
TRIML2
ELMOD2
CCDC110
MFSD8
RNF175
TRIML1
PRSS48
ANKRD37
TRIM61
HELT
GUSBP5
C4orf47
DUX4L4
GALNTL6
FRG2
C4orf51
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
FAM160A1
CLDN24
MIR1305
MIR548G
MIR3140
MIR4276
MIR3945
MIR4455
MIR4453

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.2.

Table S38. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL695P
SMAD4
ELAC1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.3.

Table S39. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BRAF
EZH2
MET
SMO
KIAA1549
CREB3L2
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
RN7SL845P
RN7SL811P
SNORA26|ENSG00000212590.1
snoU13|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13|ENSG00000239045.1
RN7SL76P
MIR3907
MIR671
IQCA1P1
CDK5
SSPO
SNORD112|ENSG00000252557.1
RN7SL521P
RNY1
RNY3
RNY4
RNY5
RN7SL569P
RN7SL72P
U3|ENSG00000199370.1
RN7SL456P
RNA5SP249
RN7SL207P
RN7SKP174
RNU6ATAC40P
OR2A9P
OR2A20P
CTAGE15
RN7SL481P
RN7SL535P
OR6W1P
TRBV30
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
OR9A1P
OR9A3P
AGK
U6|ENSG00000271932.1
RN7SL771P
RNA5SP248
snoU13|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
SNORA40|ENSG00000252188.1
snoU13|ENSG00000239123.1
SNORA51|ENSG00000201465.1
snoU13|ENSG00000238984.1
snoU13|ENSG00000239145.1
RN7SKP223
SNORD81|ENSG00000202023.1
snoU13|ENSG00000238488.1
LUZP6
C7orf73
U6|ENSG00000272393.1
SNORD46|ENSG00000201009.1
MIR29B1
MIR29A
RNA5SP246
COPG2
MIR335
snoU13|ENSG00000239044.1
snoU13|ENSG00000238336.1
RNA5SP245
RNA5SP244
TSPAN33
snoU13|ENSG00000238733.1
RN7SL306P
KCP
RN7SL81P
CALU
RNA5SP243
RNA5SP242
MIR593
MIR592
GPR37
AASS
RN7SKP277
RNA5SP241
RNA5SP240
U1|ENSG00000271739.1
NAA38
RNA5SP239
CAPZA2
snoZ185
SNORA25|ENSG00000202377.1
MIR3666
RNA5SP238
TSRM
TMEM168
IFRD1
RN7SKP187
RNA5SP237
snoU13|ENSG00000238922.1
FLJ00325
U3|ENSG00000238297.1
snoU109|ENSG00000238832.1
RNA5SP236
SNORD112|ENSG00000251911.1
RN7SL8P
LHFPL3
RN7SKP86
RN7SKP198
FAM185A
POLR2J2
MIR4467
MIR5090
MIR4285
SH2B2
SNORA48|ENSG00000252824.1
RABL5
MIR4653
RN7SKP54
MUC3A
MUC3A
RN7SL549P
RN7SL750P
SAP25
RN7SL416P
RN7SL161P
STAG3L5P
PILRB
GATS
MIR4658
MIR106B
MIR93
MIR25
AZGP1P1
SNORA40|ENSG00000222966.1
CYP3A4
snoU13|ENSG00000239133.1
MYH16
snoU13|ENSG00000238459.1
MIR3609
RN7SL13P
RN7SL478P
RN7SKP104
RN7SL252P
SHFM1
MIR591
AOC1
ACHE
AKR1B1
ARF5
ASNS
AZGP1
OPN1SW
BPGM
CALD1
CASP2
CAV1
CAV2
CFTR
CHRM2
AP1S1
CLCN1
CPA1
CPA2
CUX1
CYP3A7
CYP3A5
DLD
DLX5
DLX6
DYNC1I1
DPP6
SLC26A3
EN2
EPHA1
EPHB4
EPHB6
EPO
FLNC
GBX1
GNB2
GPR22
GRM8
MNX1
AGFG2
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LAMB1
LEP
LRCH4
MCM7
DNAJB9
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NPTX2
NRCAM
NRF1
OCM2
ORC5
SERPINE1
PAX4
PCOLCE
PDK4
SLC26A4
PIK3CG
PIP
PODXL
POLR2J
PPP1R3A
PRKAR2B
PRSS1
RELN
PSMC2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SRPK2
SSBP1
SYPL1
TAC1
TAF6
TBXAS1
TFR2
TRIP6
UBE2H
VGF
VIPR2
ZAN
WNT2
XRCC2
ZNF3
ZKSCAN1
ZSCAN21
ZYX
ST7
ARHGEF5
ZNF212
TRRAP
ZNF282
CUL1
TRIM24
BUD31
MGAM
WASL
PLOD3
DGKI
AP4M1
ATP6V1F
ASIC3
PMPCB
ATP5J2
PDIA4
UBE3C
FAM131B
DOCK4
FAM115A
DNAJB6
ABCF2
MUC12
ARPC1B
NAMPT
RASA4
SLC25A13
LRRC17
POP7
FAM3C
COG5
ZNHIT1
ARPC1A
STAG3
CPSF4
FASTK
COPS6
DUS4L
ZNF277
ABCB8
PDAP1
TFEC
LAMB4
LMTK2
PAXIP1
KLHDC10
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
ZKSCAN5
CLDN15
BRI3
TECPR1
POT1
PTCD1
CNTNAP2
TES
GIMAP2
OR2F1
FBXO24
SLC13A4
HBP1
DNAJC2
TPK1
SND1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
PILRA
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
FIS1
CPA4
WNT16
ACTL6B
PRKAG2
ZC3HC1
SRRT
MRPS33
NUB1
GPR85
TAS2R5
CHPF2
PUS7
ING3
LRRN3
ALKBH4
NCAPG2
CHCHD3
ZCWPW1
WDR60
RBM28
C7orf43
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
METTL2B
KMT2E
BAIAP2L1
BCAP29
MEPCE
TRPV5
ANKRD7
ZC3HAV1
SLC12A9
ACN9
AKR1B10
SMURF1
ACTR3B
KIAA1147
STRIP2
ESYT2
ZNF398
KMT2C
EXOC4
RINT1
GALNT11
LRRC4
LMBR1
NOM1
MOSPD3
GIGYF1
CCDC136
PARP12
CYP3A43
LRRC61
C7orf49
ZNF655
PVRIG
GCC1
GAL3ST4
PRKRIP1
CBLL1
ZNF767
CPED1
TTC26
ORAI2
JHDM1D
OR2AE1
TSC22D4
TRIM56
TMUB1
ARMC10
IMMP2L
CTTNBP2
ZNF394
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
TRIM4
ADCK2
PLXNA4
ZC3HAV1L
MYL10
CADPS2
CPA5
FOXP2
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
COL26A1
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
MUC17
RNF32
ASB15
C7orf60
CLEC2L
C7orf55
IQUB
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
RNF133
THAP5
CCDC71L
GIMAP7
ZNF467
BHLHA15
ZNF800
GIMAP1
C7orf33
ZSCAN25
FAM200A
PPP1R35
GPC2
LRWD1
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
NYAP1
CNPY4
POLR2J2
UBN2
MBLAC1
TAS2R39
TAS2R40
TAS2R41
CNPY1
FAM115C
ZNF775
ATG9B
ZNF789
LSMEM1
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
MOGAT3
FAM71F2
STRA8
WDR86
GJC3
DPY19L2P2
GATS
GSTK1
NAT16
SLC26A5
RNF148
LAMTOR4
FEZF1
FAM180A
OR2A25
OR2A5
C7orf76
PRRT4
RAB19
OR2A7
OR2A42
KPNA7
C7orf61
UFSP1
MIR182
MIR183
MIR96
SPDYE3
SPDYE2
AKR1B15
CTAGE15
OR2A2
LMOD2
ARHGEF35
GIMAP6
WEE2
POLR2J3
MIR490
ZNF862
ACTR3C
TMEM229A
CTAGE4
EFCAB10
UPK3BL
CTAGE8
RASA4B
SMKR1
ZNF783
SPDYE2B
MIR548O
MIR548F4
MTRNR2L6
TMEM178B
MIR4468
MIR5692C2
MIR5707
MIR5692A1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q22.1.

Table S40. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
TTL
ERCC3
PAX8
RN7SL283P
SNORA72|ENSG00000206901.1
RN7SKP286
NXPH2
RNA5SP105
RN7SKP141
SNORA40|ENSG00000208308.1
snoU13|ENSG00000238337.1
MIR5590
RNA5SP104
RN7SKP93
RN7SKP154
RN7SKP103
RN7SL701P
MIR4784
CYP4F31P
SCARNA4|ENSG00000252829.2
CYP4F30P
CFC1
POTEI
CYP4F43P
snoU13|ENSG00000238546.1
RNA5SP103
RN7SL206P
RNY4P7
RNA5SP102
RN7SKP102
snoU13|ENSG00000238341.1
RNU4ATAC
TMEM185B
snoU13|ENSG00000238368.1
PCDP1
RN7SL468P
RN7SL111P
HTR5BP
snoU13|ENSG00000238520.1
U3|ENSG00000212182.1
snoU13|ENSG00000239077.1
MIR4782
RPL23AP7
FAM138B
IL1A
CKAP2L
NT5DC4
snoU13|ENSG00000238951.1
RN7SL297P
LIMS3L
LIMS3|ENSG00000257207.4
LINC00116
MIR4436B2
SH3RF3
SULT1C2P1
RGPD4
GACAT1
CD8BP
PLGLA
C2orf49
POU3F3
SNORA72|ENSG00000207249.1
U3|ENSG00000199727.1
MFSD9
MIR4772
FLJ20373
CREG2
SNORD89
RN7SL548P
RN7SL360P
BIN1
BUB1
CCNT2
DARS
DBI
EN1
FHL2
GLI2
GPR17
GPR39
GYPC
HNMT
IL1B
IL1R1
IL1RN
INHBB
LCT
LIMS1
MCM6
MGAT5
MYO7B
NPAS2
NPHP1
POLR2D
PROC
PTPN4
RALB
RANBP2
RPL31
SCTR
SLC9A2
SLC20A1
SULT1C2
TSN
IL1R2
MALL
CXCR4
NCK2
MARCO
IL18RAP
IL1RL2
IL18R1
DDX18
KYNU
IL1RL1
TGFBRAP1
HS6ST1
MAP4K4
GCC2
BCL2L11
ACTR3
MERTK
MAP3K2
EDAR
TBC1D8
RABL2A
GPR45
RAB3GAP1
UBXN4
CLASP1
R3HDM1
PSD4
PTPN18
IL36RN
IL36B
IL37
IL36A
SULT1C4
C2orf27A
TFCP2L1
ARHGEF4
INSIG2
LRP1B
CCDC93
PLEKHB2
STEAP3
ACOXL
WDR33
CNOT11
SMPD4
IWS1
LIMS2
IL36G
UGGT1
DPP10
EPB41L5
SLC5A7
ANAPC1
MRPS9
SOWAHC
SAP130
MZT2B
MAP3K19
UXS1
SLC35F5
THSD7B
TMEM177
TMEM163
AMMECR1L
ZRANB3
RAB6C
POLR1B
RGPD5
CHCHD5
CCDC115
MKI67IP
C2orf40
ZC3H8
ST6GAL2
IL1F10
SFT2D3
TMEM87B
FLJ14816
CCDC74A
CCDC74B
IMP4
LIMS3|ENSG00000256977.6
TUBA3E
TUBA3D
LYPD1
CNTNAP5
FBLN7
ACMSD
FAM168B
C2orf76
TMEM182
TMEM37
CBWD2
SEPT10
CCDC138
C1QL2
FOXD4L1
AMER3
RNF149
SPOPL
CYP27C1
NCKAP5
GPR148
WASH2P
ZC3H6
SLC9A4
C2orf27B
SULT1C3
POTEE
ANKRD30BL
CFC1B
RGPD3
POTEJ
MZT2A
RGPD8
POTEF
RGPD6
RFX8
MIR663B
MIR4265
MIR4267
MIR4266
MIR3679
MIR4783
MIR5696
MIR4436B1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p24.3.

Table S41. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
IRF4
DEK
RN7SL128P
MBOAT1
ID4
RNA5SP205
snoU13|ENSG00000238458.1
RNA5SP204
STMND1
U3|ENSG00000251793.1
MIR4639
RN7SL332P
NOL7
RN7SKP204
PHACTR1
RN7SKP293
SNORA67|ENSG00000207419.1
snoU13|ENSG00000238896.1
RNA5SP203
C6orf52
GCNT6
LINC00518
RNU6ATAC21P
OFCC1
HULC
snoU13|ENSG00000251762.1
RN7SL554P
LY86
RN7SL221P
MIR3691
RMRPP2
snoU13|ENSG00000238801.1
RNA5SP202
snoU13|ENSG00000252668.1
C6ORF50
RNA5SP201
C6orf195
RN7SL352P
snoU13|ENSG00000238438.1
BMP6
BPHL
DSP
E2F3
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
HIVEP1
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
RREB1
ATXN1
SOX4
SSR1
TFAP2A
TPMT
TUBB2A
RIPK1
PRPF4B
GCM2
CD83
CDYL
EEF1E1
NUP153
RANBP9
ECI2
CAP2
FARS2
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
TBC1D7
NRN1
FAM8A1
TMEM14C
GFOD1
ELOVL2
CDKAL1
PAK1IP1
EXOC2
WRNIP1
DUSP22
LYRM4
SLC22A23
BLOC1S5
MCUR1
KIF13A
TXNDC5
TMEM14B
RIOK1
DTNBP1
ADTRP
FOXQ1
HUS1B
SNRNP48
KDM1B
RBM24
RNF182
SMIM13
SYCP2L
PXDC1
FAM217A
RNF144B
CAGE1
MYLK4
TUBB2B
NHLRC1
PSMG4
C6orf201
PPP1R3G
MIR548A1
TMEM170B
MIR4645
MIR5689
MIR5683

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q23.1.

Table S42. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PTEN
BMPR1A
FGFR2
GATA3
TLX1
NFKB2
PRF1
RET
MLLT10
NCOA4
SUFU
MIR3944
TUBGCP2
C10orf91
BNIP3
PPP2R2D
LINC00959
MIR4297
MGMT
NPS
SNORD60|ENSG00000199321.1
RNA5SP328
MIR4296
METTL10
GPR26
MIR3941
RN7SKP167
RN7SL846P
TIAL1
MIR4681
RN7SL749P
FAM45A
SNORA19|ENSG00000222588.1
SNORA19|ENSG00000207468.1
U3|ENSG00000251836.1
LINC00867
EMX2OS
PDZD8
ENO4
snoU13|ENSG00000238577.1
RN7SL384P
VWA2
NHLRC2
SNORA17|ENSG00000212589.1
MIR4295
GUCY2GP
MIR548E
RNA5SP327
RN7SKP288
RN7SL686P
snoU13|ENSG00000239125.1
SMNDC1
RN7SL450P
U4|ENSG00000272160.1
RN7SKP278
RNA5SP326
RNA5SP325
snoU13|ENSG00000238620.1
ITPRIP
MIR609
MIR936
RN7SL524P
OBFC1
C10ORF32
SFXN2
RN7SL21P
SNORD112|ENSG00000253068.1
FGF8
snoU13|ENSG00000239091.1
SNORD112|ENSG00000252844.1
LBX1
HUG1
KAZALD1
MIR608
HIF1AN
NDUFB8
LINC00263
BLOC1S2
SNORA12|ENSG00000212464.1
ERLIN1
snoU13|ENSG00000238472.1
COX15
ENTPD7
snoU13|ENSG00000238588.1
HPSE2
MIR4685
MIR1287
GOLGA7B
LINC00866
PI4K2A
EXOSC1
RNA5SP324
ZNF518A
CYP2C19
RNY4P26
PIPSL
RNA5SP323
HHEX
RN7SL644P
SNORA25|ENSG00000252993.1
LINC00502
RN7SKP143
LINC00865
MIR107
IFIT1
snoU13|ENSG00000238991.1
ANKRD22
SNORD74|ENSG00000200891.1
RN7SL78P
CFL1P1
LINC00864
LINC00863
RN7SL733P
AGAP11
U3|ENSG00000252189.1
MIR346
RNA5SP322
RN7SKP238
RN7SKP84
LINC00858
RGR
LINC00857
PLAC9
MBL1P
NUTM2E
NUTM2B
SFTPA1
SNORA71|ENSG00000201393.1
LINC00595
LINC00856
RN7SL284P
RNA5SP321
SNORA31|ENSG00000252888.1
RN7SL518P
MIR606
AP3M1
RMRPP1
GLUD1P3
BMS1P4
RNA5SP320
snoU13|ENSG00000238983.1
DNAJC9
FAM149B1
SNORA11|ENSG00000221164.1
MIR4676
SNORA36|ENSG00000200294.1
ASCC1
snoU13|ENSG00000238918.1
NODAL
NPFFR1
NEUROG3
RN7SL373P
SNORD98
snoU13|ENSG00000251926.1
SLC25A16
LINC00849
RNA5SP319
RN7SKP202
RN7SL220P
RN7SL394P
LRRTM3
snoU13|ENSG00000239000.1
snoR442|ENSG00000252203.1
MIR1296
RN7SL591P
LINC00845
LINC00948
LINC00844
RN7SKP196
snoU13|ENSG00000238970.1
SNORD2|ENSG00000238707.1
snoU13|ENSG00000238355.1
MIR548F1
RNA5SP318
MIR605
RMRPP4
RNA5SP317
LINC00843
SNORA74|ENSG00000223111.1
SNORA74|ENSG00000223182.1
RNA5SP316
FAM25D
FAM21D
PARG
C10orf53
DRGX
C10orf128
WDFY4
RNA5SP315
RN7SL527P
GLUD1P2
RNA5SP314
RNA5SP313
ASAH2C
C10orf43
ANTXRLP1
RN7SL453P
BMS1P2
RNA5SP312
AGAP10
LINC00842
GPRIN2
RN7SL248P
FAM35BP
RNA5SP311
RNA5SP310
FAM25E
RSU1P2
CEP164P1
TMEM72
LINC00841
LINC00840
LINC00619
ZNF487
U3|ENSG00000221400.1
RNU6ATAC11P
snoU13|ENSG00000238732.1
ZNF33B
ZNF37BP
CCNYL2
SEPT7P9
RN7SL314P
NAMPTL
SNORA40|ENSG00000237002.2
MIR4683
LINC00838
RN7SL398P
RN7SL847P
CCDC7
RN7SL825P
RNA5SP309
SVILP1
RN7SL63P
RN7SL241P
SNORD115|ENSG00000212411.1
MIR604
PTCHD3P1
RNA5SP308
LINC00837
RNU4ATAC6P
RN7SKP39
U3|ENSG00000222666.1
RN7SKP132
ARMC4P1
LINC00614
snoU13|ENSG00000238414.1
SNORA57|ENSG00000223027.1
LINC00264
RNA5SP307
RNA5SP306
RN7SKP220
RN7SKP241
RNA5SP305
MIR603
snoU13|ENSG00000238515.1
SNORA40|ENSG00000252049.1
RNA5SP304
RN7SKP37
RN7SKP219
MIR1915
CASC10
U3|ENSG00000251749.1
RNA5SP303
U3|ENSG00000200545.1
C10orf112
TMEM236|ENSG00000184040.7
MRC1L1
snoR442|ENSG00000251959.1
ST8SIA6
snoU13|ENSG00000238552.1
SNORA31|ENSG00000252537.1
snoU13|ENSG00000239130.1
ITGA8
NMT2
ACBD7
MEIG1
CDNF
RNA5SP302
RNA5SP301
RNA5SP300
MIR4480
RNU6ATAC39P
SNORD45|ENSG00000252438.1
RN7SL198P
RN7SL232P
snoU13|ENSG00000238900.1
U6|ENSG00000272507.1
LINC00710
SFTA1P
LINC00709
RNA5SP299
LINC00708
TAF3
LINC00707
DKFZP667F0711
MIR3155A
RN7SKP78
SNORA14
RN7SL445P
AKR1C7P
U8|ENSG00000251909.1
AKR1CL1
U8|ENSG00000239142.1
U8|ENSG00000251740.1
U8|ENSG00000239148.1
U8|ENSG00000238840.1
AKR1C1
LINC00705
LINC00704
LINC00703
LINC00702
LINC00701
LINC00700
ADARB2
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
ACADSB
ACTA2
ADAM8
ADD3
ADK
ADRA2A
ADRB1
ALOX5
ANXA8L2
ANK3
ANXA7
ANXA11
FAS
ARL3
ATP5C1
BMI1
CACNB2
CALML3
CAMK2G
CASP7
ENTPD1
CDK1
CHAT
AKR1C4
CHUK
ABCC2
COL13A1
COL17A1
KLF6
MAP3K8
CPN1
CREM
CTBP2
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
AKR1C2
DMBT1
DNA2
TRDMT1
DNTT
DOCK1
DUSP5
ECHS1
EGR2
EIF4EBP2
EMX2
ERCC6
GAD2
GDF2
GDF10
GDI2
GFRA1
GLUD1
GOT1
PRLHR
GRK5
GRID1
HABP2
HELLS
HK1
HMX2
HNRNPF
HNRNPH3
HPS1
HTR7
IDE
IDI1
IFIT2
IFIT3
IL2RA
IL15RA
INPP5A
ITGB1
ITIH2
KCNMA1
KIF5B
KIF11
ABLIM1
LIPA
MAT1A
MBL2
MKI67
MRC1
MSMB
MXI1
NDUFB8
NRAP
OAT
P4HA1
PAX2
PCBD1
PDE6C
PFKFB3
PFKP
PGAM1
PHYH
PIP4K2A
PITX3
PLAU
PNLIP
PNLIPRP1
PNLIPRP2
PPA1
PPP1R3C
PPP3CB
NPY4R
SRGN
PRKCQ
PRKG1
MAPK8
HTRA1
PSAP
PSD
PTPRE
ALDH18A1
RBP3
RBP4
RGS10
RPS24
RSU1
SCD
CXCL12
SFRP5
SFTPD
FBXW4
SLC18A2
SLC18A3
SLIT1
SNCG
SUPV3L1
SVIL
TACR2
TAF5
TCF7L2
ZEB1
TECTB
TFAM
TLL2
UBE2D1
UROS
VCL
VDAC2
VIM
WNT8B
XPNPEP1
ZNF22
ZNF32
ZNF33A
ZNF33B
ZNF37A
STAM
CUBN
CCDC6
SHOC2
ADAM12
ZNF239
FZD8
UTF1
CUL2
NDST2
LIPF
PRPF18
AKR1C3
EIF3A
GBF1
NRP1
LDB1
CDC123
SGPL1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
SMC3
NEURL
BUB3
DDX21
PTPLA
LGI1
NOLC1
DLG5
PTER
GSTO1
CHST3
BAG3
VPS26A
MINPP1
SPAG6
KIF20B
SEC24C
SH3PXD2A
FAM53B
USP6NL
SLK
BMS1
SPOCK2
RHOBTB1
DCLRE1A
ABI1
FRAT1
PPIF
ACTR1A
OPTN
NET1
NPM3
MICU1
NEBL
PITRM1
GLRX3
RPP30
RPP38
DPYSL4
TACC2
SORBS1
CELF2
NRG3
MGEA5
YME1L1
ZMYND11
PRDX3
ADIRF
VAX1
C10orf10
ATE1
POLR3A
ZWINT
LDB3
NUDT5
SEC23IP
ECD
RAB11FIP2
CPEB3
ANKRD26
INPP5F
WDR37
ZNF365
MSRB2
SEPHS1
RAB18
DKK1
KIN
NT5C2
DIP2C
PDCD11
SORCS3
ZSWIM8
WAPAL
PPRC1
FAM175B
LARP4B
RRP12
TBC1D12
DNMBP
CSTF2T
FRAT2
SIRT1
COMMD3
KAT6B
TSPAN15
GTPBP4
PDSS1
IFIT5
BAMBI
DPCD
SEC31B
NUDT13
UPF2
ATRNL1
HERC4
PTPN20B
C10orf137
LRIT1
TCTN3
KIAA1279
C10orf12
ANKRD2
CNNM1
MYOF
ANKRD1
GHITM
PALD1
PDCD4
VENTX
R3HCC1L
POLL
CTNNA3
BLNK
A1CF
NRBF2
KCNIP2
CUZD1
CALY
MRPS16
CALHM2
CUTC
HSPA14
PLCE1
DUSP13
WAC
CHST15
ACSL5
CALML5
PANK1
FXYD4
MYO3A
CCSER2
APBB1IP
ANKRD16
EXOC6
FAM35A
DDIT4
CCNJ
MARCH5
ZRANB1
TTC40
NSMCE4A
DNAJB12
CNNM2
WBP1L
FAM208B
C10orf118
CRTAC1
ARMC4
MTPAP
CEP55
SEC61A2
LRRC20
CWF19L1
OLAH
SLC29A3
RNLS
PI4K2A
MCM10
CSGALNACT2
H2AFY2
DHTKD1
RUFY2
FRMD4A
WDR11
FAM178A
FAM21B
CCAR1
OGDHL
DHX32
CISD1
TDRD1
KIAA1217
PARD3
DNAJC12
ASAH2
BCCIP
C10orf2
SAR1A
TM9SF3
PRTFDC1
CAMK1D
ZMIZ1
ZNF248
AS3MT
GPR158
STAMBPL1
ARHGAP21
KIAA1462
GPAM
KIAA1598
FAM160B1
SFMBT2
SEMA4G
ARHGAP22
MYOZ1
PLEKHA1
AVPI1
FAM204A
CDH23
LHPP
PBLD
C10orf54
MMS19
DNAJC1
NOC3L
IKZF5
DCLRE1C
ZDHHC6
PCDH15
CUEDC2
DDX50
FBXL15
OR13A1
C10orf76
SUV39H2
C10orf68
ECHDC3
ASB13
HPS6
MMRN2
TMEM180
TUBAL3
MCMBP
THNSL1
SYNPO2L
C10orf95
PLEKHS1
PDZD7
C10orf88
FAM188A
UBTD1
BICC1
TMEM254
HKDC1
WDR96
TET1
LRRC27
EPC1
TNKS2
ITIH5
TRIM8
TSPAN14
SFXN3
SLC25A28
ELOVL3
AKR1E2
FAM107B
CCDC3
MARVELD1
SYT15
RASSF4
C10orf11
PCGF6
ARID5B
LOXL4
ZDHHC16
FAM213A
DYDC2
PCGF5
GPR123
LZTS2
PHYHIPL
LCOR
MRPL43
LYZL1
AFAP1L2
PLA2G12B
MYPN
PYROXD2
USMG5
LINC00839
ZNF503
AIFM2
ADO
FBXO18
ATAD1
PLXDC2
MASTL
ARHGAP19
RBM17
KNDC1
MCU
ANKRD30A
ACBD5
IDI2
MTG1
CDHR1
BBIP1
FANK1
OPALIN
SYCE1
ZFAND4
ARHGAP12
OPN4
HOGA1
UCN3
SORCS1
C10orf71
PRAP1
ZNF511
CHCHD1
MSS51
TTC18
C10orf90
BTBD16
FAM24A
PSTK
ZNF488
PIK3AP1
MORN4
ZFYVE27
MMP21
COMTD1
FRA10AC1
AGAP4
C10orf32
LYZL2
GSTO2
SFR1
CALHM3
CLRN3
ANAPC16
PNLIPRP3
SFXN4
CPXM2
ADAMTS14
C10orf129
SAMD8
LIPJ
TRUB1
MPP7
FRMPD2
VTI1A
DYDC1
EIF5AL1
HECTD2
FGFBP3
C10orf82
CACUL1
HSD17B7P2
USP54
SLC35G1
CCDC147
FAM170B
FUT11
OIT3
PWWP2B
ANTXRL
PPAPDC1A
VSTM4
PAOX
FAM24B
C10orf107
TMEM26
ZCCHC24
ENKUR
ARMC3
UNC5B
STOX1
C10orf35
TYSND1
ZNF25
GJD4
CCNY
RTKN2
TBATA
ATOH7
OTUD1
ZNF438
SLC16A9
FAM13C
MARCH8
C10orf25
ZNF485
RASGEF1A
REEP3
JMJD1C
UCMA
C10orf111
FAM171A1
SLC39A12
NSUN6
ARL5B
BEND7
IPMK
FAM21C
EBF3
PROSER2
CALHM1
CASC2
PTF1A
TCERG1L
C10orf67
HSPA12A
SGMS1
FUOM
JAKMIP3
STK32C
RBM20
C10orf40
MKX
C10orf126
FFAR4
KCNK18
DUPD1
LIPM
CYP26C1
NANOS1
LRIT2
HMX3
EBLN1
PTCHD3
CCDC172
C10orf113
SKIDA1
C10orf115
LRRC37A6P
FAM21A
SH2D4B
C10orf99
SLC16A12
CC2D2B
ARMS2
TEX36
C1QL3
LINC00200
BMS1P5
C10orf120
FOXI2
GOLGA7B
C10orf85
C10orf105
C10orf62
AGAP6
PRR26
C10orf55
IFIT1B
FRG2B
LRRC18
SPRN
MIR146B
MIR202
AGAP9
FAM196A
FAM25A
LIPK
LIPN
FAM25C
PTPN20A
ANXA8
TIMM23B
AGAP7
ASAH2B
TMEM236|ENSG00000148483.7
MIR607
BMS1P1
ANXA8L1
NUTM2A
NUTM2D
AGAP8
AGAP5
SFTPA2
TLX1NB
MIR938
C10orf131
FAM25B
FAM25G
KLLN
TIMM23
MTRNR2L7
MIR1265
MIR1307
MIR2110
MIR548Q
MIR4293
MIR378C
MIR3157
MIR4294
MTRNR2L5
MIR3924
MIR3611
MIR3663
MIR4680
MIR4682
MIR4484
MIR4675
MIR548AK
MIR5100
LINC00601
PGBD3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q21.2.

Table S43. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
KTN1
GPHN
NIN
CCNB1IP1
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SNORA7|ENSG00000222604.1
ISCA2
MIR4709
RN7SL530P
LIN52
ENTPD5
snoU13|ENSG00000238330.1
ACOT4
C14orf169
RN7SL586P
snoU13|ENSG00000238972.1
RN7SL683P
SNORD56B
RN7SL77P
ADAM20P1
SYNJ2BP
ADAM21P1
SNORA11|ENSG00000221060.1
SLC10A1
CCDC177|ENSG00000267909.1
CCDC177|ENSG00000255994.1
ERH
RN7SL224P
RN7SL108P
RN7SL706P
RN7SL213P
U3|ENSG00000252792.1
RN7SL369P
ATP6V1D
MIR4706
FNTB
ZBTB25
U3|ENSG00000200693.1
WDR89
SCARNA20|ENSG00000252800.1
RN7SL540P
PPP2R5E
GPHB5
LINC00644
LINC00643
SNORD112|ENSG00000252380.1
SIX1
U3|ENSG00000253014.1
SIX6
MIR5586
JKAMP
GPR135
ACTR10
RN7SL598P
C14orf37
RN7SKP99
NAA30
RN7SL461P
LINC00520
RPL13AP3
TBPL2
MIR4308
RNU6ATAC9P
RN7SL588P
ERO1L
RNA5SP385
LINC00640
LINC00519
SNORA70|ENSG00000201376.1
TMX1
snoU83B
RN7SL452P
CDKL1
MIR4504
RN7SKP193
ARF6
RN7SL2
RN7SL3
RNU6ATAC30P
RPL36AL
RN7SL1
RNA5SP384
SNORD112|ENSG00000251824.1
LINC00648
SNORA25|ENSG00000251735.1
LINC00871
SNORD127
SNORD58
snoU13|ENSG00000238501.1
SNORA31|ENSG00000251858.1
FBXO33
LINC00639
LINC00517
SNORA42|ENSG00000200385.1
TTC6
MIR4503
SLC25A21
RN7SKP257
DPPA3P2
RN7SKP21
PTCSC3
snoU13|ENSG00000238718.1
SNORA31|ENSG00000253059.1
KIAA0391
RN7SL660P
GPR33
MIR624
BNIP3P1
LINC00645
SNORD37|ENSG00000212270.1
TM9SF1
RNA5SP383
DHRS4L1
LINC00596
RN7SKP205
MIR208B
MIR208A
PABPN1
C14orf164
SNORA73|ENSG00000252114.1
SNORD41|ENSG00000212302.1
OR6J1
TRAC
TRAJ1
TRAJ2
TRAJ3
TRAJ4
TRAJ5
TRAJ6
TRAJ7
TRAJ8
TRAJ9
TRAJ10
TRAJ11
TRAJ12
TRAJ13
TRAJ14
TRAJ16
TRAJ17
TRAJ18
TRAJ19
TRAJ20
TRAJ21
TRAJ22
TRAJ23
TRAJ24
TRAJ25
TRAJ26
TRAJ27
TRAJ28
TRAJ29
TRAJ30
TRAJ31
TRAJ32
TRAJ33
TRAJ34
TRAJ35
TRAJ36
TRAJ37
TRAJ38
TRAJ39
TRAJ40
TRAJ41
TRAJ42
TRAJ43
TRAJ44
TRAJ45
TRAJ46
TRAJ47
TRAJ48
TRAJ49
TRAJ50
TRAJ52
TRAJ53
TRAJ54
TRAJ56
TRAJ57
TRAJ58
TRAJ59
TRAJ61
TRDV3
TRDC
TRDJ3
TRDJ2
TRDJ4
TRDJ1
TRDD3
TRDD2
TRDD1
TRDV2
TRAV41
TRAV40
TRAV39
TRAV36DV7
TRAV35
TRAV34
TRAV30
TRAV29DV5
TRAV27
TRAV25
TRAV24
TRDV1
TRAV23DV6
TRAV22
TRAV21
TRAV20
TRAV19
TRAV18
TRAV17
TRAV16
TRAV14DV4
TRAV10
TRAV7
TRAV6
TRAV5
TRAV4
TRAV3
TRAV2
RN7SL650P
SNORD8
SNORD9
LINC00641
RNASE8
RN7SL189P
PNP
RNA5SP382
RPPH1
SNORD126
SNORA79|ENSG00000222489.1
TTC5
OR11H7
RNA5SP381
RNA5SP380
OR4Q2
snoU13|ENSG00000238492.1
MED15P6
LINC00516
MED15P1
ACTN1
ACYP1
ANG
APEX1
ARG2
ARHGAP5
BCL2L2
BMP4
ZFP36L1
CDKN3
CEBPE
CFL2
CMA1
LTB4R
CTSG
DAD1
COCH
DLST
EIF2S1
ESR2
FKBP3
FOXG1
FOS
FUT8
GCH1
GMFB
GPX2
GZMH
GZMB
HIF1A
FOXA1
HNRNPC
HSPA2
LGALS3
LTBP2
MAX
MGAT2
CTAGE5
MAP3K9
MMP14
ALDH6A1
MNAT1
MTHFD1
MYH6
MYH7
NEDD8
NFATC4
NFKBIA
NOVA1
NRL
OTX2
OXA1L
PAX9
PCK2
PGF
PIGH
PNN
POLE2
PPM1A
PRKCH
PRKD1
PSEN1
PSMA3
PSMA6
PSMB5
PSMC6
PSME1
PSME2
PTGDR
PTGER2
ABCD4
PYGL
RABGGTA
RAD51B
ARID4A
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
RPS29
RTN1
SALL2
SRSF5
SLC8A3
SNAPC1
SOS2
SPTB
SRP54
SSTR1
STYX
TEP1
TGM1
DPF3
GEMIN2
NUMB
ADAM21
ADAM20
DCAF5
EIF2B2
AP1G2
SLC7A7
NEMF
PNMA1
CPNE6
AKAP6
AKAP5
RGS6
KIAA0391
KIAA0247
KIAA0586
DLGAP5
AREL1
TOX4
REC8
MED6
PARP2
CNIH
DHRS2
EFS
IRF9
PRMT5
SEC23A
VTI1B
BATF
TM9SF1
NPC2
EXOC5
CGRRF1
EDDM3A
DHRS4
ACOT2
TMED10
FERMT2
RIPK3
AP4S1
WDHD1
BAZ1A
MAP4K5
SUPT16H
NID2
ATG14
ZBTB1
ACIN1
PCNX
DAAM1
SAMD4A
TTLL5
FAM179B
SYNE2
SCFD1
KHNYN
SLC7A8
ZFYVE26
TTC9
KLHDC2
HECTD1
HEATR5A
NGDN
LRP10
PLEKHG3
SIPA1L1
DCAF4
TINF2
PLEK2
TIMM9
OR10G3
OR10G2
OR4E2
MLH3
ATP5S
KCNH5
CIDEB
CHMP4A
STXBP6
STRN3
SLC39A2
COQ6
EMC9
ATL1
FCF1
RDH11
ZNF219
COX16
GMPR2
SLC22A17
DACT1
MBIP
DHRS7
C14orf166
SIX4
ZFYVE1
GNG2
KLHL28
TMEM260
HAUS4
PPP2R3C
PRPF39
C14orf119
FBXO34
RNF31
RBM23
DNAAF2
C14orf105
EXD2
VRTN
MIS18BP1
SLC39A9
G2E3
FLVCR2
OSGEP
GPATCH2L
ARHGEF40
AP5M1
EAPP
YLPM1
METTL3
LTB4R2
SDR39U1
RPGRIP1
PELI2
RHOJ
NDRG2
GALNT16
PLEKHH1
NYNRIN
TXNDC16
TRMT5
HOMEZ
CHD8
FANCM
ZNF410
RBM25
SNX6
SAV1
C14orf93
ABHD4
NPAS3
SMOC1
EDDM3B
MPP5
CDH24
PCNXL4
METTL17
IL25
GNPNAT1
THTPA
OR4K5
OR4K1
METTL21D
ZC2HC1C
IPO4
L2HGDH
CCDC176
NUBPL
DCAF11
DDHD1
OR4K15
SGPP1
DNAL1
RPS6KL1
SYT16
FSCB
BRMS1L
JPH4
RNASE7
INSM2
RAB2B
AJUBA
ZFHX2
PAPLN
LRRC16B
PPP1R3E
TMEM55B
CHURC1
ELMSAN1
NEK9
MAPK1IP1L
EGLN3
DTD2
IFT43
L3HYPDH
TRIM9
DHRS1
CMTM5
MIA2
C14orf28
TRAPPC6B
RNASE11
TPPP2
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
LRR1
KLHDC1
FRMD6
SOCS4
JDP2
KLHL33
RPL10L
RDH12
MIPOL1
PPP1R36
SLC38A6
ABHD12B
PTGR2
FAM161B
MDP1
LRFN5
FAM71D
TMEM229B
CLEC14A
FITM1
REM2
TMEM30B
MDGA2
NOP9
SPTSSA
ADCY4
C14orf183
RALGAPA1
SFTA3
C14orf182
GPR137C
PROX2
TSSK4
FAM177A1
DHRS4L2
C14orf39
RNASE10
VSX2
OR6S1
SLC35F4
LRRC9
RAB15
C14orf23
TOMM20L
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
HEATR4
PLEKHD1
POTEG
OR11H12
RNASE13
LINC00238
OR4Q3
OR4M1
RNASE12
ACOT1
ACOT6
POTEM
TMEM253
CBLN3
SYNDIG1L
MIR625
CCDC175
MIR548H1
MIR4307
MIR548Y
MIR4505
MIR4708
MIR4707
MIR5694
MIR5580
LINC00609

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q14.2.

Table S44. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BTG1
CDK4
DDIT3
MDM2
NACA
HMGA2
WIF1
LUM
LINC00615
RNA5SP365
LINC00936
KITLG
RNA5SP364
MKRN9P
SNORA3|ENSG00000221148.1
MIR4699
MIR618
MIR617
PTPRQ
RN7SKP261
RNA5SP363
PAWR
RN7SL696P
MIR1252
snoU13|ENSG00000238769.1
RN7SKP172
PHLDA1
RN7SL734P
SNORA70|ENSG00000251893.2
GLIPR1
U8|ENSG00000201809.1
RAB21
SNORA17|ENSG00000212461.1
MYRFL
RN7SL804P
SLC35E3
SNORA70G
DYRK2
CAND1
snoU13|ENSG00000238528.1
RN7SKP166
TMBIM4
RNA5SP362
RPSAP52
RNU6ATAC42P
snoU13|ENSG00000238592.1
MIR548C
SNORD83
XPOT
snoU13|ENSG00000238440.1
RPS11P6
AVPR1A
LDHAL6CP
snoU13|ENSG00000238475.1
SNORD112|ENSG00000252883.1
SNORA19|ENSG00000251822.1
RN7SKP65
MIR26A2
snoU13|ENSG00000238436.1
RN7SL312P
MIR1228
HBCBP
RDH16
SNORA48|ENSG00000212383.1
RN7SL809P
SNORD59A
RBMS2
RNF41
RN7SL770P
APOF
ATP2B1
ATP5B
CDK2
CPM
CS
CSRP2
CYP27B1
DGKA
DCN
EPYC
DUSP6
ERBB3
B4GALNT1
GLI1
GNS
IFNG
INHBC
KCNC2
KIF5A
LRP1
LYZ
MARS
METTL1
MIP
MYF5
MYF6
MYL6
MYO1A
PPP1R12A
NAB2
NAP1L1
CNOT2
NTS
PA2G4
PRIM1
PTPRB
PTPRR
RAB5B
RAP1B
RPL41
RPS26
TSPAN31
SHMT2
PMEL
SMARCC2
STAT2
STAT6
SUOX
SYT1
TAC3
TSPAN8
YEATS4
ALX1
PPFIA2
LGR5
HSD17B6
GALNT4
LIN7A
TIMELESS
RASSF9
SLC16A7
ZBTB39
PAN2
USP15
TSFM
CTDSP2
TMEM5
CNPY2
DCTN2
CCT2
AVIL
PTGES3
FRS2
OS9
CPSF6
KERA
KRR1
BAZ2A
IRAK3
NXPH4
GPR182
R3HDM2
MON2
TMEM194A
TBC1D30
ESYT1
ZDHHC17
GRIP1
LEMD3
MGAT4C
METTL21B
GLS2
KCNMB4
CCDC59
TBK1
TRHDE
IL22
IL23A
TMBIM4
SLC6A15
TMEM19
IL26
MDM1
NDUFA4L2
NUP107
PPM1H
SRGAP1
ARHGAP9
IKZF4
TBC1D15
SLC26A10
NABP2
ACSS3
BBS10
PIP4K2C
CEP290
THAP2
INHBE
LRRIQ1
METTL25
LLPH
CAPS2
ZC3H10
NAV3
C12orf29
XRCC6BP1
HELB
MARCH9
COQ10A
MBD6
OSBPL8
ARHGEF25
C12orf56
AGAP2
RAB3IP
SDR9C7
LRIG3
TPH2
MYL6B
GLIPR1L2
TSPAN19
BEST3
E2F7
C12orf66
TMTC2
TMTC3
C12orf50
DTX3
ZFC3H1
CCER1
STAC3
MSRB3
C12orf79
GLIPR1L1
POC1B
OTOGL
RASSF3
ANKRD52
SLC39A5
SPRYD4
C12orf61
DPY19L2
FAM19A2
LRRC10
MIRLET7I
ATXN7L3B
MIR616

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q43.

Table S45. Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FH
PGBD2
LYPD8
OR2T7
OR2AJ1
TRIM58
OR1C1
OR14K1
OR14A2
OR2W5
RNA5SP82
MIR3916
ZNF670
SNORA25|ENSG00000252011.1
SNORD112|ENSG00000252495.1
RN7SKP55
RN7SL148P
MIR4677
RN7SKP12
RNA5SP81
CHRM3
MTRNR2L11
ZP4
SNORA25|ENSG00000252290.1
MIR4428
RN7SKP195
snoU13|ENSG00000252638.1
MIR4753
SNORA14B
RN7SL668P
RNY4P16
LINC00184
U8|ENSG00000212144.1
MIR4671
MIR4427
ACTN2
ADSS
CHML
LYST
GNG4
HNRNPU
KCNK1
LGALS8
MTR
NID1
RGS7
RYR2
TARBP1
TBCE
GPR137B
ZNF124
KMO
EXO1
GGPS1
TOMM20
CEP170
AKT3
ZBTB18
SDCCAG8
RBM34
OPN3
AHCTF1
OR2M4
OR2L2
OR2T1
DESI2
SCCPDH
ARID4B
KIF26B
HEATR1
ZNF692
ERO1LB
FMN2
ZNF695
TFB2M
GREM2
SMYD3
ZNF669
ZNF672
PCNXL2
SH3BP5L
OR2L5
OR2G3
OR2G2
OR2C3
EFCAB2
MLK4
ZNF496
NLRP3
COX20
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
OR2B11
WDR64
EDARADD
SLC35F3
B3GALNT2
GCSAML
CNST
PLD5
C1orf100
OR2T6
C1orf101
OR2L13
OR14A16
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
COA6
C1orf229
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MAP1LC3C
OR13G1
MT1HL1
MIR1537
MIR3123
MIR3124
MIR3916

Arm-level results

Table 3. Get Full Table Arm-level significance table - 23 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 1300 | 0.03 | -3.39 | 1 | 0.35 | 3.12 | 0.0122
1q | 1195 | 0.09 | -2.75 | 1 | 0.26 | 0.732 | 0.999
2p | 624 | 0.18 | -2.25 | 1 | 0.22 | -1.5 | 0.999
2q | 967 | 0.15 | -2.12 | 1 | 0.20 | -1.1 | 0.999
3p | 644 | 0.17 | -2.23 | 1 | 0.27 | -0.526 | 0.999
3q | 733 | 0.20 | -1.52 | 1 | 0.28 | -0.176 | 0.999
4p | 289 | 0.45 | 2.02 | 0.0521 | 0.22 | -1.91 | 0.999
4q | 670 | 0.41 | 2.27 | 0.0297 | 0.21 | -1.44 | 0.999
5p | 183 | 0.69 | 6.36 | 6.7e-10 | 0.26 | -1.08 | 0.999
5q | 905 | 0.64 | 7.74 | 6.98e-14 | 0.19 | -1.03 | 0.999
6p | 710 | 0.23 | -1.03 | 1 | 0.28 | -0.085 | 0.999
6q | 556 | 0.24 | -1.29 | 1 | 0.30 | -0.186 | 0.999
7p | 389 | 0.56 | 4.52 | 1.06e-05 | 0.14 | -2.63 | 0.999
7q | 783 | 0.57 | 5.97 | 6.99e-09 | 0.14 | -1.97 | 0.999
8p | 338 | 0.43 | 1.79 | 0.0834 | 0.28 | -0.942 | 0.999
8q | 551 | 0.49 | 3.43 | 0.000825 | 0.23 | -1.2 | 0.999
9p | 301 | 0.28 | -1.11 | 1 | 0.30 | -0.765 | 0.999
9q | 700 | 0.36 | 1.35 | 0.19 | 0.19 | -1.67 | 0.999
10p | 253 | 0.32 | -0.449 | 1 | 0.18 | -2.72 | 0.999
10q | 738 | 0.33 | 0.797 | 0.416 | 0.16 | -2.28 | 0.999
11p | 509 | 0.08 | -4.16 | 1 | 0.28 | -0.611 | 0.999
11q | 975 | 0.08 | -3.35 | 1 | 0.28 | 0.567 | 0.999
12p | 339 | 0.75 | 8.19 | 2.28e-15 | 0.19 | -1.53 | 0.999
12q | 904 | 0.74 | 10.1 | 0 | 0.15 | -1.28 | 0.999
13q | 560 | 0.12 | -2.93 | 1 | 0.46 | 3.13 | 0.0122
14q | 938 | 0.29 | 0.611 | 0.505 | 0.26 | 0.0145 | 0.999
15q | 810 | 0.16 | -2.16 | 1 | 0.27 | -0.201 | 0.999
16p | 559 | 0.58 | 5.36 | 2.12e-07 | 0.17 | -1.97 | 0.999
16q | 455 | 0.55 | 4.61 | 8.26e-06 | 0.12 | -2.86 | 0.999
17p | 415 | 0.09 | -3.88 | 1 | 0.38 | 1.02 | 0.902
17q | 972 | 0.08 | -3.26 | 1 | 0.31 | 1.06 | 0.902
18p | 104 | 0.11 | -3.78 | 1 | 0.44 | 1.47 | 0.717
18q | 275 | 0.09 | -3.93 | 1 | 0.41 | 1.36 | 0.717
19p | 681 | 0.66 | 7.44 | 5.06e-13 | 0.15 | -1.86 | 0.999
19q | 935 | 0.60 | 7.13 | 4.05e-12 | 0.13 | -1.88 | 0.999
20p | 234 | 0.56 | 4.05 | 7.55e-05 | 0.22 | -1.76 | 0.999
20q | 448 | 0.56 | 4.72 | 5.38e-06 | 0.10 | -3.13 | 0.999
21q | 258 | 0.41 | 1.26 | 0.212 | 0.25 | -1.45 | 0.999
22q | 564 | 0.07 | -3.3 | 1 | 0.55 | 4.97 | 1.4e-05
Xp | 418 | 0.56 | 4.33 | 2.33e-05 | 0.35 | 0.338 | 0.999
Xq | 668 | 0.53 | 4.52 | 1.06e-05 | 0.33 | 0.626 | 0.999

Methods & Data
Input
Description

- Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

- Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).

- Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.

- CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End

- Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.

- Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.

- Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.

- Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.

- Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.

- Confidence Level: Confidence level used to calculate the region containing a driver.

- Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.

- Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).

- Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.

- Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

List of inputs used for this run of GISTIC2. All files listed should be included in the archived results.

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/ACC-TP/14516395/GDAC_MergeDataFiles_12177564/ACC-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

- Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt

- Reference Genome = /xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.mat

- CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

- Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 90 Input Tumor Samples.

Tumor Sample Names
TCGA-OR-A5J1-01A-11D-A29H-01
TCGA-OR-A5J2-01A-11D-A29H-01
TCGA-OR-A5J3-01A-11D-A29H-01
TCGA-OR-A5J4-01A-11D-A29H-01
TCGA-OR-A5J5-01A-11D-A29H-01
TCGA-OR-A5J6-01A-31D-A29H-01
TCGA-OR-A5J7-01A-11D-A29H-01
TCGA-OR-A5J8-01A-11D-A29H-01
TCGA-OR-A5J9-01A-11D-A29H-01
TCGA-OR-A5JA-01A-11D-A29H-01

Figure 3. Segmented copy number profiles in the input data

Output
All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The all lesions file summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

Region Data

Columns 1-9 present the data about the significant regions as follows:

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

8. Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

9. Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

Each of the analyzed samples is represented in one of the columns following the lesion data (columns 10 through end). The data contained in these columns varies slightly by section of the file. The first section can be identified by the key given in column 9 - it starts in row 2 and continues until the row that reads 'Actual Copy Change Given.' This section contains summarized data for each sample. A '0' indicates that the copy number of the sample was not amplified or deleted beyond the threshold amount in that peak region. A '1' indicates that the sample had low-level copy number aberrations (exceeding the low threshold indicated in column 9), and a '2' indicates that the sample had high-level copy number aberrations (exceeding the high threshold indicated in column 9).The second section can be identified the rows in which column 9 reads 'Actual Copy Change Given.' The second section exactly reproduces the first section, except that here the actual changes in copy number are provided rather than zeroes, ones, and twos.The final section is similar to the first section, except that here only broad events are included. A 1 in the samples columns (columns 10+) indicates that the median copy number of the sample across the entire significant region exceeded the threshold given in column 9. That is, it indicates whether the sample had a geographically extended event, rather than a focal amplification or deletion covering little more than the peak region.

Amplification Genes File (amp_genes.conf_##.txt, where ## is the confidence level)

The amp genes file contains one column for each amplification peak identified in the GISTIC analysis. The first four rows are:

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

These rows identify the lesion in the same way as the all lesions file.The remaining rows list the genes contained in each wide peak. For peaks that contain no genes, the nearest gene is listed in brackets.

Deletion Genes File (del_genes.conf_##.txt, where ## is the confidence level)

The del genes file contains one column for each deletion peak identified in the GISTIC analysis. The file format for the del genes file is identical to the format for the amp genes file.

Gistic Scores File (scores.gistic)

The scores file lists the Q values [presented as -log10(q)], G scores, average amplitudes among aberrant samples, and frequency of aberration, across the genome for both amplifications and deletions. The scores file is viewable with the Genepattern SNPViewer module and may be imported into the Integrated Genomics Viewer (IGV).

Segmented Copy Number (raw_copy_number.{fig|pdf|png} )

The segmented copy number is a pdf file containing a colormap image of the segmented copy number profiles in the input data.

Amplification Score GISTIC plot (amp_qplot.{fig|pdf|png|v2.pdf})

The amplification pdf is a plot of the G scores (top) and Q values (bottom) with respect to amplifications for all markers over the entire region analyzed.

Deletion Score GISTIC plot (del_qplot.{fig|pdf|png|v2.pdf})

The deletion pdf is a plot of the G scores (top) and Q values (bottom) with respect to deletions for all markers over the entire region analyzed.

Tables (table_{amp|del}.conf_##.txt, where ## is the confidence level)

Tables of basic information about the genomic regions (peaks) that GISTIC determined to be significantly amplified or deleted. These describe three kinds of peak boundaries, and list the genes contained in two of them. The region start and region end columns (along with the chromosome column) delimit the entire area containing the peak that is above the significance level. The region may be the same for multiple peaks. The peak start and end delimit the maximum value of the peak. The extended peak is the peak determined by robust, and is contained within the wide peak reported in {amp|del}_genes.txt by one marker.

Broad Significance Results (broad_significance_results.txt)

A table of per-arm statistical results for the data set. Each arm is a row in the table. The first column specifies the arm and the second column counts the number of genes known to be on the arm. For both amplification and deletion, the table has columns for the frequency of amplification or deletion of the arm, and a Z score and Q value.

Broad Values By Arm (broad_values_by_arm.txt)

A table of chromosome arm amplification levels for each sample. Each row is a chromosome arm, and each column a sample. The data are in units of absolute copy number -2.

All Data By Genes (all_data_by_genes.txt)

A gene-level table of copy number values for all samples. Each row is the data for a gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. The copy number values in the table are in units of (copy number -2), so that no amplification or deletion is 0, genes with amplifications have positive values, and genes with deletions are negative values. The data are converted from marker level to gene level using the extreme method: a gene is assigned the greatest amplification or the least deletion value among the markers it covers.

Broad Data By Genes (broad_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only broad events with lengths greater than the broad length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

Focal Data By Genes (focal_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only focal events with lengths greater than the focal length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

All Thresholded By Genes (all_thresholded.by_genes.txt)

A gene-level table of discrete amplification and deletion indicators at for all samples. There is a row for each gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. A table value of 0 means no amplification or deletion above the threshold. Amplifications are positive numbers: 1 means amplification above the amplification threshold; 2 means amplifications larger to the arm level amplifications observed for the sample. Deletions are represented by negative table values: -1 represents deletion beyond the threshold; -2 means deletions greater than the minimum arm-level deletion observed for the sample.

Sample Cutoffs (sample_cutoffs.txt)

A table of the per-sample threshold cutoffs (in units of absolute copy number -2) used to distinguish the high level amplifications (+/-2) from ordinary amplifications (+/-1) in the all_thresholded.by_genes.txt output file. The table contains three columns: the sample identifier followed by the low (deletion) and high (amplification) cutoff values. The cutoffs are calculated as the minimum arm-level amplification level less the deletion threshold for deletions and the maximum arm-level amplification plus the amplification threshold for amplifications.

Focal Input To Gistic (focal_input.seg.txt)

A list of copy number segments describing just the focal events present in the data. The segment amplification/deletion levels are in units of (copy number -2), with amplifications positive and deletions negative numbers. This file may be viewed with IGV.

Gene Counts vs. Copy Number Alteration Frequency (freqarms_vs_ngenes.{fig|pdf})

An image showing the correlation between gene counts and frequency of copy number alterations.

Confidence Intervals (regions_track.conf_##.bed, where ## is the confidence level)

A file indicating the position of the confidence intervals around GISTIC peaks that can be loaded as a track in a compatible viewer browser such as IGV or the UCSC genome browser.

GISTIC

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. It takes segmented copy number ratios as input, separates arm-level events from focal events, and then performs two tests: (i) identifies significantly amplified/deleted chromosome arms; and (ii) identifies regions that are significantly focally amplified or deleted. For the focal analysis, the significance levels (Q values) are calculated by comparing the observed gains/losses at each locus to those obtained by randomly permuting the events along the genome to reflect the null hypothesis that they are all 'passengers' and could have occurred anywhere. The locus-specific significance levels are then corrected for multiple hypothesis testing. The arm-level significance is calculated by comparing the frequency of gains/losses of each arm to the expected rate given its size. The method outputs genomic views of significantly amplified and deleted regions, as well as a table of genes with gain or loss scores. A more in depth discussion of the GISTIC algorithm and its utility is given in [1], [3], and [5].

CNV Description

Regions of the genome that are prone to germ line variations in copy number are excluded from the GISTIC analysis using a list of germ line copy number variations (CNVs). A CNV is a DNA sequence that may be found at different copy numbers in the germ line of two different individuals. Such germ line variations can confound a GISTIC analysis, which finds significant somatic copy number variations in cancer. A more in depth discussion is provided in [6]. GISTIC currently uses two CNV exclusion lists. One is based on the literature describing copy number variation, and a second one comes from an analysis of significant variations among the blood normals in the TCGA data set.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[2] GISTIC version 1
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[4] GISTIC version 2
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)
[7] The Sanger Institute: Cancer Gene Census
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